AlignACE version 2.2 July 7, 1998 AlignACE -jMSS.orf -y -e Parameter values: expect = 10 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 YDL107W 300 bp YDL107W mss2 1-1056 cox1 pre-mRNA splicing factor #2 YDR194C 600 bp YDR194C MSS116 1-1995 Mitochondrial RNA helicase of the DEAD box family #3 YDR208W 600 bp YDR208W MSS4 1-2340 Phosphatidylinositol 4-phosphate kinase #4 YLR203C 309 bp YLR203C mss51 1-1311 Protein involved in maturation of COX1 and COB mRNA #5 YMR023C 300 bp YMR023C MSS1 1-1581 putative mitochondrial GTPase #6 YMR164C 489 bp YMR164C MSS11 1-2277 Predicted 758 amino acid polypeptide with poly-glutamine and poly-asparagine domains #7 YPR134W 341 bp YPR134W MSS18 1-807 Protein involved in splicing intron a15beta of COX1 Motif number 1 TGGTGTTGAATTTTAACTCTTTTCCATCATTAT 1 181 1 TTTTACTTTT 0.716664 -120 ATGGAATTCGTTTTTAGATTTTAACAACAACAA 1 212 1 TTTTTTTTTA 0.856549 -89 GATCAGATATTTCTTGCTTTTGTTTTCGTTTTC 1 272 0 TTCTTTTTGT 0.731554 -29 TGCTTGTAGGTTTTTGAGCTTTAACCTCACTTA 2 43 1 TTTTTCTTTA 0.929171 -558 GTTCTTTTCATTTTTCTTTTTGACGGCGGCAGT 3 22 1 TTTTTTTTGA 0.830474 -579 CATCCATTCCTTTCTTTTTTTTTTTAACCTGTG 3 364 0 TTTCTTTTTT 0.95902 -237 GTCCTTGTTTTTTCTTTGCTTGTCCCTCCGTAT 3 460 0 TTTCTCTTGT 0.976843 -141 CTATTTTTTGTTTCTGTCCTTGTTTTTTCTTTG 3 475 0 TTTCTCTTGT 0.976843 -126 GGTTGTAGTTTTTTTACACTTTATAAGCGCAGA 4 226 1 TTTTTCTTTA 0.929171 -84 GTAGGATACATTTTTAAACTTTTATTAATGAAA 5 34 0 TTTTTCTTTT 0.972492 -267 ACATTTATGTTTTCTATACTTCTTCAAAGTCTT 5 65 1 TTTCTCTTCT 0.890224 -236 GACTCGTCCATTTTTTATTTTTTTGGCTAACTA 5 172 1 TTTTTTTTTT 0.941491 -129 TAAGTAACAATTTTTCAATTTTATTTAAGAAAA 6 77 1 TTTTTTTTTA 0.856549 -413 TCTTTTTTTTTTCCTTCTCTTTTCTTAAATAAA 6 96 0 TTCCTCTTTT 0.913892 -394 ATCAAAAAATTTTCTTCTTTTTTTTTTCCTTCT 6 111 0 TTTCTTTTTT 0.95902 -379 AATAGAAATCTTTCTGGTCTTTTCTACTATGGT 6 361 0 TTTCTCTTTT 0.980922 -129 CTAAAATATGTTTCTCTTTTTGTATTTGCTTTT 7 50 1 TTTCTTTTGT 0.950495 -292 CTAAATCTCCTTTCTTCGCTTGTATATATGCGT 7 177 1 TTTCTCTTGT 0.976843 -165 TCCAGGCAGATTTTTCGGCTTTTTTTACCAGCT 7 224 1 TTTTTCTTTT 0.972492 -118 ***** ***** Masking position 10 Map Score: 24.3937 Number of sites scoring better than the average of aligned sites = 3464 Number in coding regions = 1577 Number in noncoding regions = 1887 Number of orfs with sites within 600 bp upstream = 1269 Fraction of orfs with sites within 600 bp upstream = 0.203823 Motif number 2 GTTATGCTTGTTTTGTTCTGCCTCCAACAGTG 2 189 1 TTTTTTCTCC 0.978919 -412 AGGTTGCTAATTTGCTTTTTTGAAATAAAACA 2 410 0 TTTGTTTTTG 0.810249 -191 TATAGGAAAATTTTATTCTTTCTATAATATCA 2 500 0 TTTTTTCTTC 0.977173 -101 CTCTATGTTCTTTTCATTTTTCTTTTTGACGG 3 16 1 TTTTATTTTC 0.759728 -585 TTAACCTGTGTTTTGTTTTCCCAGAATGGGCG 3 342 0 TTTTTTTTCC 0.975662 -259 TTCCTTTCTTTTTTTTTTTAACCTGTGTTTTG 3 359 0 TTTTTTTTAC 0.838703 -242 GTTGTCACGCTTTTGTTATTTCCACCTCTATC 3 418 0 TTTTTTATTC 0.943607 -183 TCCCTCCGTATTTGCTTCTTTGTTGTCACGCT 3 439 0 TTTGTTCTTG 0.831832 -162 TTGTTTTTTCTTTGCTTGTCCCTCCGTATTTG 3 457 0 TTTGTTGTCC 0.88854 -144 GTTCCTATTTTTTGTTTCTGTCCTTGTTTTTT 3 480 0 TTTGTTCTTC 0.969743 -121 AATTTTCTTCTTTTTTTTTTCCTTCTCTTTTC 6 105 0 TTTTTTTTCC 0.975662 -385 TCGTTTACCTTTTTCTTCTATCAAAAAATTTT 6 131 0 TTTTTTCTTC 0.977173 -359 ACTATGGTGATTTTATTATACCCCTCCTCTTC 6 337 0 TTTTTTATCC 0.947785 -153 GTGTGACTCTTTTGGTTTTTCCCTTTGGTATC 6 402 1 TTTGTTTTCC 0.967756 -88 TCATGCACCTTTTTCTTATTTCACTGCAGTTT 6 461 0 TTTTTTATTC 0.943607 -29 TGTGCACTGATTTTCTCTTTTCCTTGGTTATG 7 319 0 TTTTTCTTTC 0.824142 -23 **** **** ** Masking position 9 Map Score: 15.5126 Number of sites scoring better than the average of aligned sites = 3581 Number in coding regions = 1301 Number in noncoding regions = 2280 Number of orfs with sites within 600 bp upstream = 1511 Fraction of orfs with sites within 600 bp upstream = 0.242692 Motif number 3 ACGAAAACAAAAGCAAGAAATATCTGATCT 1 276 1 AAGCAAGAAA 0.795916 -25 AAAAACCTACAAGCAAAGGCACAAGGAAAT 2 28 0 AAGCAAAGGC 0.944413 -573 AAGCATCCATAAGTAAAGACACTTTGAGGT 2 438 0 AAGTAAAGAC 0.825565 -163 TCAGAGTGGCAAGAAAATACCAGAGTTGCA 2 567 1 AAGAAAATAC 0.940814 -34 TAAAAAAAAAAAGAAAGGAATGGATGGGGA 3 371 1 AAGAAAGGAA 0.88372 -230 GACAACAAAGAAGCAAATACGGAGGGACAA 3 444 1 AAGCAAATAC 0.928855 -157 GGGACAAGCAAAGAAAAAACAAGGACAGAA 3 467 1 AAGAAAAAAC 0.958801 -134 GCACATTCATAAGCAAGAGAGTACGAAACC 3 520 1 AAGCAAGAGA 0.684126 -81 AAGCGGCTCGAAGAAAATAATCCAAAGGAG 4 144 1 AAGAAAATAA 0.853805 -166 AATTTTATTTAAGAAAAGAGAAGGAAAAAA 6 93 1 AAGAAAAGAG 0.964141 -397 TTTTTGATAGAAGAAAAAGGTAAACGATGA 6 136 1 AAGAAAAAGG 0.903186 -354 ATCACCATAGTAGAAAAGACCAGAAAGATT 6 358 1 TAGAAAAGAC 0.761174 -132 GCAGTGAAATAAGAAAAAGGTGCATGATAA 6 466 1 AAGAAAAAGG 0.903186 -24 TTCCCCACTGAAGAAAAAAGATTGCATCTA 7 11 1 AAGAAAAAAG 0.943816 -331 ATTTAATCAAAAGCAAATACAAAAAGAGAA 7 61 0 AAGCAAATAC 0.928855 -281 TATACAAGCGAAGAAAGGAGATTTAGGCTC 7 173 0 AAGAAAGGAG 0.937232 -169 ********** Masking position 5 Map Score: 11.7543 Number of sites scoring better than the average of aligned sites = 3314 Number in coding regions = 1973 Number in noncoding regions = 1341 Number of orfs with sites within 600 bp upstream = 971 Fraction of orfs with sites within 600 bp upstream = 0.155959 Motif number 4 AAAACGAAAACAAAAGCAAGAAATATCTGA 1 273 1 CAAAAGCAAG 0.811443 -28 ATAGACCCGCCAAAAGAAACCGTTGGTGTG 2 116 1 CAAAAGAAAC 0.914413 -485 CAATACAGTACAAAAGAGTTATGCTTGTTT 2 172 1 CAAAAGAGTT 0.701436 -429 ATTTTCCTATAAAAAGAAGGGAAGTATTGA 2 521 1 AAAAAGAAGG 0.728103 -80 GGCATTGGTGAAAAGGCGCCTTGAAGCACG 3 63 1 AAAAGGCGCC 0.877959 -538 AACGGATATACAAAAGCGACACGTCGTCTG 3 291 0 CAAAAGCGAC 0.972962 -310 GGTTAAAAAAAAAAAGAAAGGAATGGATGG 3 368 1 AAAAAGAAAG 0.732049 -233 GTGGAAATAACAAAAGCGTGACAACAAAGA 3 425 1 CAAAAGCGTG 0.923136 -176 AGCGCATGATAAAAAGAGCCCTTTCCCCAT 4 108 0 AAAAAGAGCC 0.967118 -202 ATGCGCTACGAAAAAGCGGCTCGAAGAAAA 4 131 1 AAAAAGCGGC 0.956398 -179 GAAAATAATCCAAAGGAGTCTGACAAGAGA 4 156 1 CAAAGGAGTC 0.881589 -154 CGTCAGGTGAAAAAAGCGGCCAAGAGGCAA 6 280 1 AAAAAGCGGC 0.956398 -210 AGGGAAAAACCAAAAGAGTCACACAGGATT 6 396 0 CAAAAGAGTC 0.96755 -94 GAAAAATTGACAAAAGAACCGGGAGATACC 6 428 0 CAAAAGAACC 0.932227 -62 AAGCAAATACAAAAAGAGAAACATATTTTA 7 51 0 AAAAAGAGAA 0.64286 -291 AAAAGCTGGTAAAAAAAGCCGAAAAATCTG 7 230 0 AAAAAAAGCC 0.608551 -112 ********** Masking position 4 Map Score: 8.14722 Number of sites scoring better than the average of aligned sites = 2449 Number in coding regions = 1758 Number in noncoding regions = 691 Number of orfs with sites within 600 bp upstream = 593 Fraction of orfs with sites within 600 bp upstream = 0.0952457 Motif number 5 CCACCACCAAGTGACCCGTCTTCAATAAAAAT 1 48 1 GTACCCGTCT 0.96887 -253 GCTACTGTTTGTCTCCCCTCATATTGTTGTTG 1 236 0 GTTCCCCTCT 0.86995 -65 CTACCGCTCTGTATCACGTCGGCACACCAACG 2 136 0 GTTCACGTCG 0.993786 -465 CGGCGCCAGCGTTTTTCGTCAGTTTTTCTCAA 2 273 0 GTTTTCGTCG 0.860657 -328 TTCGGTCCGGGTGACACGTCCGCCGTGCTTCA 3 84 0 GTACACGTCG 0.993773 -517 GTTGAGTGGAGTGTCACCTCAGACGACGTGTC 3 272 1 GTTCACCTCG 0.971727 -329 ATATACAAAAGCGACACGTCGTCTGAGGTGAC 3 284 0 GCACACGTCT 0.975682 -317 ATCTACTATTGTCTCTTGTCAGACTCCTTTGG 4 165 0 GTTCTTGTCG 0.860656 -145 GTTGCCACATGTCTTCAAATTGGTT 5 4 1 GCACATGTCT 0.848998 -297 TACCGACTACGCCACACGCCCGATTTGTATTG 5 98 0 GCACACGCCG 0.93883 -203 GCTGCAACAGGTATTACGTCAGGTGAAAAAAG 6 264 1 GTTTACGTCG 0.956933 -226 TTAAAAAATATTTACACGTCTTTCTCTAAACT 7 121 0 TTACACGTCT 0.838551 -221 ** ******* * Masking position 10 Map Score: 6.82155 Number of sites scoring better than the average of aligned sites = 400 Number in coding regions = 277 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 6 GTCGTGTATCGTGATATATCGTGATTTACAA 2 309 1 GTATATATCG 0.982144 -292 TTTACAACTGGTAATATATAGATGAATACCG 2 333 1 GTATATATAG 0.97376 -268 GTAGGCTGGAGTGATATATGGCACTGTTTTA 2 386 1 GTATATATGG 0.993263 -215 CGTAAAAGACGTTATATATGGGTTAGTTAGC 5 197 0 GTATATATGG 0.993263 -104 CTTAGAGAATGTTATATATGGTTAATAAGTA 5 272 1 GTATATATGG 0.993263 -29 ** ******** Masking position 6 Map Score: 4.58816 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 25 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 TTGTTTTCGTTTTCGTCTGCTACTGTTTGT 1 256 0 TTTCGTCTGC 0.983996 -45 TCCTTTCGATTTCCTTGTGCCTTTGCTTGT 2 20 1 TTCCTTGTGC 0.935626 -581 AAAAGAAACCGTTGGTGTGCCGACGTGATA 2 127 1 GTTGGTGTGC 0.959073 -474 TTATGCTTGTTTTGTTCTGCCTCCAACAGT 2 190 1 TTTGTTCTGC 0.897612 -411 ATTCTCGTGATTTCGTGTGCAACCAATGGA 3 189 1 TTTCGTGTGC 0.993184 -412 TGGCATTCACTTAAGTGTGCAGTATGGGGA 4 85 1 TTAAGTGTGC 0.873232 -225 AGCAAGCGAGTTTCGTGTGCGTATAGAAAA 6 237 0 TTTCGTGTGC 0.993184 -253 ********** Masking position 6 Map Score: 3.29493 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 158 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 8 TCTGAGACACCATAGTGGCCATCAATACTTC 2 541 0 CAAGTGGCCA 0.983454 -60 TATGGTGTCTCAGAGTGGCAAGAAAATACCA 2 558 1 CAAGTGGCAA 0.991843 -43 AAGAAAATACCAGAGTTGCACGTTAGGCTGA 2 577 1 CAAGTTGCAC 0.885717 -24 ATGAAAAGAACATAGAGGACAA 3 2 0 CAAGAGGACA 0.959999 -599 GGGAATGGGACAGAGAGGAAAGATAGAGGTG 3 397 1 CAAGAGGAAA 0.980039 -204 AGCGTGACAACAAAGAAGCAAATACGGAGGG 3 439 1 CAAGAAGCAA 0.976115 -162 AAAAAAGCGGCCAAGAGGCAATGCCGAAATA 6 289 1 CCAGAGGCAA 0.972224 -201 ATAAAATCACCATAGTAGAAAAGACCAGAAA 6 353 1 CAAGTAGAAA 0.915764 -137 TAGTGTCATTCATAGATGCAATCTTTTTTCT 7 22 0 CAAGATGCAA 0.976115 -320 ** ******** Masking position 4 Map Score: 6.97437 Number of sites scoring better than the average of aligned sites = 588 Number in coding regions = 472 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 9 TCAAGGCGGTATAAAAAATCGATGATATTCG 2 246 0 ATAAAAAATG 0.966822 -355 AAGGACAGAAACAAAAAATAGGAACAAGAAG 3 487 1 ACAAAAAATG 0.960057 -114 AGCCAAAAAAATAAAAAATGGACGAGTCCGG 5 169 0 ATAAAAAATG 0.966821 -132 ATGGATCGTTATAAATAATATTCGGCTACAA 6 17 0 ATAAATAATT 0.644536 -473 TTAAATAAAATTGAAAAATTGTTACTTAGTA 6 74 0 TTGAAAAATG 0.920391 -416 TTTTCTTCTATCAAAAAATTTTCTTCTTTTT 6 122 0 TCAAAAAATT 0.793459 -368 CTGCAGTTTAACGAAAAATTGACAAAAGAAC 6 439 0 ACGAAAAATG 0.921561 -51 TTGCTTTTGATTAAATAATGGTCAATTTGCG 7 75 1 TTAAATAATG 0.881995 -267 TAAATATTTTTTAAAAAATTGATACTGCTCT 7 139 1 TTAAAAAATG 0.959436 -203 ********* * Masking position 5 Map Score: 1.62716 Number of sites scoring better than the average of aligned sites = 947 Number in coding regions = 641 Number in noncoding regions = 306 Number of orfs with sites within 600 bp upstream = 232 Fraction of orfs with sites within 600 bp upstream = 0.0372631 Motif number 10 ATCGATGATATTCGATTGAGGCACTTGTTAA 2 229 0 TTCGATTAGG 0.96273 -372 GCTACTTCTCTTCTGTTTCGGTCCGGGTGAC 3 101 0 TTCTGTTCGG 0.959675 -500 AGAATGCACGTTGGATTTCGGGCATCCTATA 3 146 0 TTGGATTCGG 0.985085 -455 CGAAAGGCGGTTGAGTTCCAGCCAAGACGAG 4 38 0 TTGAGTTCAG 0.791599 -272 CACGCCCGATTTGTATTGAAGACTTTGAAGA 5 85 0 TTGTATTAAG 0.789801 -216 AGGTCTCCGGTTCGATTCCGGACTCGTCCAT 5 152 1 TTCGATTCGG 0.985093 -149 TATACACGCATTGTATTTCGGCATTGCCTCT 6 302 0 TTGTATTCGG 0.976751 -188 TATCGCAACCTTCAATTAAGGTTATCACATT 7 268 0 TTCAATTAGG 0.919773 -74 ******* *** Masking position 6 Map Score: 0.939992 Number of sites scoring better than the average of aligned sites = 396 Number in coding regions = 323 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 11 ACCAAGTGACCCGTCTTCAATAAAAATACG 1 53 1 CCGTCTTCAA 0.887112 -248 ATTTTTTATACCGCCTTGAGAAAAACTGAC 2 258 1 CCGCCTTGAG 0.993769 -343 GTTTCATTCTCCGTCTGTAGTGATATTATA 2 480 1 CCGTCTGTAG 0.949029 -121 GCGGCAGTTTCCGCCTGGCATTGGTGAAAA 3 47 1 CCGCCTGGCA 0.972196 -554 TGGTGAAAAGGCGCCTTGAAGCACGGCGGA 3 68 1 GCGCCTTGAA 0.93689 -533 TGGAACTCAACCGCCTTTCGCTCTTGATAT 4 49 1 CCGCCTTTCG 0.98556 -261 AACCAAAGGCCCGCCCTTAGTAGTTGACCA 4 200 0 CCGCCCTTAG 0.968953 -110 ********** Masking position 5 Map Score: 0.303562 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 238 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 12 AAAACAAGACGCATCAAGAAGTTTATTTGT 1 150 0 GCATCAAGAA 0.948176 -151 GAAATCGAAAGGACCAAGAAAG 2 3 0 GGACCAAGAA 0.962572 -598 ACAAGCAAAGGCACAAGGAAATCGAAAGGA 2 20 0 GCACAAGGAA 0.842252 -581 AACATGCATTGCTACAAGTAGTAGAGCGCA 3 229 0 GCTACAAGTA 0.932141 -372 ACAAAAAATAGGAACAAGAAGTAGCACATT 3 497 1 GGAACAAGAA 0.955151 -104 CGAAAAAGCGGCTCGAAGAAAATAATCCAA 4 139 1 GCTCGAAGAA 0.897025 -171 ATAATATTCGGCTACAAGAATCT 6 4 0 GCTACAAGAA 0.974041 -486 CTCGCTTGCTGCAACAGGTATTACGTCAGG 6 257 1 GCAACAGGTA 0.925808 -233 ********** Masking position 6 Map Score: 0.416383 Number of sites scoring better than the average of aligned sites = 1013 Number in coding regions = 787 Number in noncoding regions = 226 Number of orfs with sites within 600 bp upstream = 201 Fraction of orfs with sites within 600 bp upstream = 0.032284 Motif number 13 ********** No masking Map Score: 4.55701e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 14 ********** No masking Map Score: 4.55701e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 15 ********** No masking Map Score: 4.55701e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0